To execute, use the run() method. Input and output files are specified in the arguments of run() (see "FILES"):

$samt->run( -bam => "mysam.sam", -out => "mysam.bam" );

OPTIONS

samtools is complex, with many subprograms (commands) and command-line options and file specs for each. This module attempts to provide commands and options comprehensively. You can browse the choices like so:

Reasonably mnemonic names have been assigned to the single-letter command line options. These are the names returned by available_parameters, and can be used in the factory constructor like typical BioPerl named parameters.

FILES

When a command requires filenames, these are provided to the run() method, not the constructor (new()). To see the set of files required by a command, use available_parameters('filespec') or the alias filespec():

Support

rather than to the module maintainer directly. Many experienced and reponsive experts will be able look at the problem and quickly address it. Please include a thorough description of the problem with code and data examples if at all possible.

Reporting Bugs

Report bugs to the Bioperl bug tracking system to help us keep track of the bugs and their resolution. Bug reports can be submitted via the web:

http://redmine.open-bio.org/projects/bioperl/

AUTHOR - Mark A. Jensen

Email maj -at- fortinbras -dot- us

APPENDIX

The rest of the documentation details each of the object methods. Internal methods are usually preceded with a _